How jarninggau/projectsvr works
ProjectSVR is an R package for mapping single-cell RNA-seq query cells onto reference atlases. The documented workflow is to prepare a reference/model, project query data, and inspect or further analyze the projection. The README also describes feature selection, signature scoring, pseudotime prediction, and cell-type classification. Source excerpts were unavailable, so links are limited to documented relationships; the listed R paths identify existing source files but do not establish internal call wiring.
Main entry points: wrappers.R Map query · objects.R Create reference · cnmf.R Feature selection · projection.R Project query
Components 17
Reference modeling
- Create reference
R/objects.R - Reference model
R/objects.R - Feature selection
R/cnmf.R
Query mapping
- Project query
R/projection.R - Map query
R/wrappers.R - Refine projection
R/projection.R - Cell projection
R/objects.R
Cell analysis
- Label transfer
R/label_transfer.R - Signature scoring
R/signature_score.R - Cell-type classifier
R/wrappers.R - Pseudotime prediction
R/projection.R - Projection quality
R/projection.R
Results and plots
- Projection plots
R/visualization.R
Other components
- Analyst
- Reference atlas
- Query data
- Python cNMF
Connections 18
- Analyst → Create reference: builds
- Reference atlas → Create reference: provides data
- Create reference → Reference model: creates
- Analyst → Feature selection: selects features
- Feature selection → Python cNMF: optionally invokes
- Analyst → Map query: maps query
- Map query → Project query: projects with
- Map query → Reference model: uses model
- Map query → Query data: uses query
- Project query → Cell projection: produces
- Analyst → Refine projection: refines
- Analyst → Label transfer: transfers labels
- Analyst → Signature scoring: scores signatures
- Analyst → Cell-type classifier: predicts types
- Analyst → Pseudotime prediction: predicts pseudotime
- Analyst → Projection quality: assesses quality
- Analyst → Projection plots: plots results
- Cell projection → Projection plots: visualizes